Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,064,161 G→A 7.6% L42L (CTG→CTA) ‡ yccE → uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,064,1610GA 7.6% 207.7 / 7.3 66L42L (CTG→CTA) ‡yccEuncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (31/30);  new base A (2/3);  total (33/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.70e-01

TTTATAGACGCTATATATGGGTAGTAATATACATGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGAAATGCAGA  >  NC_000913/1064020‑1064267
                                                                                                                                             |                                                                                                          
tttATAGACGCTATATATGGGTAGTAATATACATGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAATAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGgtgtgt                                                                                                      >  4:782779/1‑148 (MQ=255)
        cGCTATATATGGGTAGTAATATACATGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCg                                                                                              <  3:782779/148‑1 (MQ=255)
                      agtaATATACATGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCg                                                                                              <  3:71932/134‑1 (MQ=255)
                      agtaATATACATGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCg                                                                                              >  4:71932/1‑134 (MQ=255)
                           tataCATGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTgg                                                                                                           <  2:840222/116‑1 (MQ=255)
                           tataCATGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTgg                                                                                                           >  1:840222/1‑116 (MQ=255)
                                 tGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGa                                                                                  <  2:649364/135‑1 (MQ=255)
                                 tGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGa                                                                                  >  1:649364/1‑135 (MQ=255)
                                  ggAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGtttt                                                                                                   <  3:87553/117‑1 (MQ=255)
                                  ggAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGtttt                                                                                                   >  4:87553/1‑117 (MQ=255)
                                     aTTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATg                                                                                                <  4:689074/117‑1 (MQ=255)
                                     aTTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATg                                                                                                >  3:689074/1‑117 (MQ=255)
                                     aTTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACaa                                                                                     >  4:374809/1‑128 (MQ=255)
                                     aTTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACaa                                                                                     <  3:374809/128‑1 (MQ=255)
                                                 gCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTtata                                                                                        <  1:179090/113‑1 (MQ=255)
                                                 gCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTtata                                                                                        >  2:179090/1‑113 (MQ=255)
                                                 gCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATa                                                     >  3:394366/1‑148 (MQ=255)
                                                      taatTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACGCTGatgt                                                                                                        >  2:807067/1‑92 (MQ=255)
                                                      taatTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACgtaaagtaaa                                                                <  1:483944/132‑1 (MQ=255)
                                                      taatTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACgtaaagtaaa                                                                >  2:483944/1‑132 (MQ=255)
                                                      taatCATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGgtgt                                                                                                        <  1:807067/92‑1 (MQ=255)
                                                              tGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTc                                                  >  4:637722/1‑138 (MQ=255)
                                                              tGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTc                                                  <  3:637722/138‑1 (MQ=255)
                                                                     ggCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGtttt                                                                                                   <  2:10809/82‑1 (MQ=255)
                                                                     ggCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGtttt                                                                                                   >  1:10809/1‑82 (MQ=255)
                                                                         tGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAg                                                                            <  3:100719/101‑1 (MQ=255)
                                                                         tGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAg                                                                            >  4:100719/1‑101 (MQ=255)
                                                                          ggAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACgtaaagtaaa                                                                >  2:880290/1‑112 (MQ=255)
                                                                          ggAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACgtaaagtaaa                                                                <  1:880290/112‑1 (MQ=255)
                                                                           gAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATg                                              <  3:648686/129‑1 (MQ=255)
                                                                           gAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATg                                              >  4:648686/1‑129 (MQ=255)
                                                                                  ataAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGa                                                                                  <  2:372897/86‑1 (MQ=255)
                                                                                  ataAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGa                                                                                  >  1:372897/1‑86 (MQ=255)
                                                                                                  aaaaaaaTCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGa                                                             >  2:532206/1‑91 (MQ=255)
                                                                                                  aaaaaaaTCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGa                                                             <  1:532206/91‑1 (MQ=255)
                                                                                                  aaaaaaaTCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGaa         >  1:520783/1‑143 (MQ=255)
                                                                                                  aaaaaaaTCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGaa         <  2:520783/143‑1 (MQ=255)
                                                                                                   aaaaaaTCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGaa                                                            <  1:521973/91‑1 (MQ=255)
                                                                                                   aaaaaaTCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGaa                                                            >  2:521973/1‑91 (MQ=255)
                                                                                                            aaCATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAaga                                                          <  3:824409/84‑1 (MQ=255)
                                                                                                            aaCATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAaga                                                          >  4:824409/1‑84 (MQ=255)
                                                                                                             aCATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGAAATGCAg   >  1:839742/1‑138 (MQ=255)
                                                                                                             aCATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGAAATGCAg   <  2:839742/138‑1 (MQ=255)
                                                                                                              cATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGa                   <  4:994225/121‑1 (MQ=255)
                                                                                                              cATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGa                   >  3:994225/1‑121 (MQ=255)
                                                                                                              cATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTg              <  3:1109526/126‑1 (MQ=255)
                                                                                                              cATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTg              >  4:1109526/1‑126 (MQ=255)
                                                                                                                 atTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCAc                             >  2:644544/1‑108 (MQ=255)
                                                                                                                 atTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCAc                             <  1:644544/108‑1 (MQ=255)
                                                                                                                   tCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTg                                          <  3:793756/93‑1 (MQ=255)
                                                                                                                   tCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTg                                          >  4:793756/1‑93 (MQ=255)
                                                                                                                   tCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATc                               >  1:296615/1‑104 (MQ=255)
                                                                                                                   tCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATc                               <  2:296615/104‑1 (MQ=255)
                                                                                                                          agCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAag                                                           >  4:1060392/2‑69 (MQ=255)
                                                                                                                          agCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAag                                                           <  3:1060392/68‑1 (MQ=255)
                                                                                                                            cTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGATGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAAtg                                     >  2:864944/1‑89 (MQ=255)
                                                                                                                            cTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAAtg                                     <  1:864944/89‑1 (MQ=255)
                                                                                                                              ttttGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCa                                                <  1:1041573/76‑1 (MQ=255)
                                                                                                                              ttttGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCa                                                >  2:1041573/1‑76 (MQ=255)
                                                                                                                                   aaaaCACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGaa         <  3:890613/110‑1 (MQ=255)
                                                                                                                                   aaaaCACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGaa         >  4:890613/1‑110 (MQ=255)
                                                                                                                                    aaaCACACCAGTGTGTTTTATGCGGTTATACAGTGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAAtg                                     >  3:971076/1‑81 (MQ=255)
                                                                                                                                    aaaCACACCAGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAAtg                                     <  4:971076/81‑1 (MQ=255)
                                                                                                                                    aaaCACACCAGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGAAATGCAGa  >  1:551338/1‑116 (MQ=255)
                                                                                                                                    aaaCACACCAGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGAAATGCAGa  <  2:551338/116‑1 (MQ=255)
                                                                                                                                      acacacCAGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGaa         <  2:462697/107‑1 (MQ=255)
                                                                                                                                         cacTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTg              >  3:224709/1‑99 (MQ=255)
                                                                                                                                         cacTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTg              <  4:224709/99‑1 (MQ=255)
                                                                                                                                             |                                                                                                          
TTTATAGACGCTATATATGGGTAGTAATATACATGGAATTAGTTGCACTGCAAATAATTATTTGAAACAGGCCTGGAACGATATAAAAAATGAGTACGAAAAAAATCAAACATATTCAATCACGCTTTTTGAAAACACACTGGTGTGTTTTATGCGGTTATACAATGAACTCAGACGTAAAGTAAATGAAGAGGATACTCCATGTCTGGAATGTGAATCACTAGAAAAAGAATTTGAGGAAATGCAGA  >  NC_000913/1064020‑1064267

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A